BMRB Entry 30955

Name: SARS-CoV-2 Nucleocapsid N-terminal domain (N-NTD) protein
Published: 2022-06-03

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PDB ID: 7sd4
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30955
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

SARS-CoV-2 Nucleocapsid N-terminal domain (N-NTD) protein

Deposition date:

2021-09-29

Original release date:

2022-06-03

Authors:

Sarkar, S.; Runge, B.; Russell, R.; Calero, D.; Zeinalilathori, S.; Quinn, C.; Lu, M.; Calero, G.; Gronenborn, A.; Polenova, T.

Citation:

Citation: Sarkar, Sucharita; Runge, Brent; Russell, Ryan; Movellan, Kumar Tekwani; Calero, Daniel; Zeinalilathori, Somayeh; Quinn, Caitlin; Lu, Manman; Calero, Guillermo; Gronenborn, Angela; Polenova, Tatyana. "Atomic-Resolution Structure of SARS-CoV-2 Nucleocapsid Protein N-Terminal Domain" J. Am. Chem. Soc. 144, 10543-10555 (2022).
PubMed: 35638584

Assembly members:

Assembly members:
entity_1, polymer, 136 residues, 14994.733 Da.

Natural source:

Natural source: Common Name: 2019-nCoV, SARS-CoV-2 Taxonomy ID: 2697049 Superkingdom: Viruses Kingdom: not available Genus/species: Betacoronavirus HCoV-SARS

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SRRPQGLPNNTASWFTALTQ HGKEDLKFPRGQGVPINTNS SPDDQIGYYRRATRRIRGGD GKMKDLSPRWYFYYLGTGPE AGLPYGANKDGIIWVATEGA LNTPKDHIGTRNPANNAAIV LQLPQGTTLPKGFYAE

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	595
15N chemical shifts	147
1H chemical shifts	133

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 136 residues - 14994.733 Da.

1

SER

ARG

PRO

GLN

GLY

LEU

PRO

ASN

2

THR

ALA

SER

TRP

PHE

THR

ALA

LEU

THR

GLN

3

HIS

GLY

LYS

GLU

ASP

LEU

LYS

PHE

PRO

ARG

4

GLY

GLN

GLY

VAL

PRO

ILE

ASN

THR

ASN

SER

5

SER

PRO

ASP

GLN

ILE

GLY

TYR

ARG

6

ARG

ALA

THR

ARG

ILE

ARG

GLY

ASP

7

GLY

LYS

MET

LYS

ASP

LEU

SER

PRO

ARG

TRP

8

TYR

PHE

TYR

LEU

GLY

THR

GLY

PRO

GLU

9

ALA

GLY

LEU

PRO

TYR

GLY

ALA

ASN

LYS

ASP

10

GLY

ILE

TRP

VAL

ALA

THR

GLU

GLY

ALA

11

LEU

ASN

THR

PRO

LYS

ASP

HIS

ILE

GLY

THR

12

ARG

ASN

PRO

ALA

ASN

ALA

ILE

VAL

13

LEU

GLN

LEU

PRO

GLN

GLY

THR

LEU

PRO

14

LYS

GLY

PHE

TYR

ALA

GLU

Samples:

sample_1: N-NTD, [U-100% 13C; U-100% 15N], 30 mg/mL

sample_conditions_1: ionic strength: 50 mM; pH: 6.2; pressure: 1 atm; temperature: 298.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D CORD 25 ms	sample_1	isotropic	sample_conditions_1
2D CORD 100 ms	sample_1	isotropic	sample_conditions_1
2D CORD 250 ms	sample_1	isotropic	sample_conditions_1
2D CORD 500 ms	sample_1	isotropic	sample_conditions_1
2D NCACX 25 ms	sample_1	isotropic	sample_conditions_1
2D NCOCX 25 ms	sample_1	isotropic	sample_conditions_1
2D CP RFDR	sample_1	isotropic	sample_conditions_1
2D hNH HETCOR	sample_1	isotropic	sample_conditions_1
2D hCH HETCOR	sample_1	isotropic	sample_conditions_1
3D hCANH	sample_1	isotropic	sample_conditions_1
3D hCONH	sample_1	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CcpNmr Analysis, Stevens TJ, Fogh RH, Boucher W, Higman VA, Eisenmenger F, Bardiaux B, van Rossum BJ, Oschkinat H, Laue ED - data analysis

NMRFAM-SPARKY, Lee W, Tonelli M, Markley JL - chemical shift assignment

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMR spectrometers:

Bruker AVANCE III 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks